BIMSBbioinfo · Artur-man · May 22, 2024 · May 21, 2024 · May 21, 2024 · May 21, 2024
diff --git a/R/annotation.R b/R/annotation.R
@@ -297,6 +297,7 @@ annotateSpatialData <- function(object, label = "annotation", assay = NULL, use.
           } else {
             spatialpoints <- rownames(metadata)
           }
+
           new_label <- rep("undefined", length(spatialpoints))
           names(new_label) <- spatialpoints
           result_list <- list()
@@ -339,4 +340,3 @@ annotateSpatialData <- function(object, label = "annotation", assay = NULL, use.
     shiny::runApp(shiny::shinyApp(ui, server))
   }
 }
-
diff --git a/R/visualization.R b/R/visualization.R
@@ -170,7 +170,10 @@ vrSpatialPlot <- function(object, group.by = "Sample", plot.segments = FALSE, gr
       return(gg[[1]] + theme(legend.position=legend.loc))
     }
   } else {
-    gg + theme(legend.position=legend.loc)
+    for(i in 1:length(assay_names)){
+      gg[[i]] <- gg[[i]] + theme(legend.position=legend.loc)
+    }
+    return(gg)
   }
 }
 
@@ -259,6 +262,7 @@ vrSpatialPlotSingle <- function(assay, metadata, group.by = "Sample", plot.segme
   } else {
     coords[[group.by]] <- metadata[,group.by]
   }
+
   if(!is.null(group.ids)){
     if(length(setdiff(group.ids,  coords[[group.by]])) > 0){
       # warning("Some groups defined in group.ids does not exist in group.by!")
@@ -358,6 +362,7 @@ vrSpatialPlotSingle <- function(assay, metadata, group.by = "Sample", plot.segme
 
         # add points
         if(n.tile == 0){
+
           g <- g +
             geom_point(mapping = aes_string(x = "x", y = "y", fill = group.by, color = group.by), coords, shape = cell.shape, size = rel(pt.size), alpha = alpha) +
             scale_fill_manual(values = colors, labels = names(colors), drop = FALSE, limits = names(colors)) +
@@ -591,7 +596,10 @@ vrSpatialFeaturePlot <- function(object, features, group.by = "label", plot.segm
       return(gg[[1]] + theme(legend.position=legend.loc))
     }
   } else {
-    return(gg + theme(legend.position=legend.loc))
+    for(i in 1:(length(features)*length(assay_names))){
+      gg[[i]] <- gg[[i]] + theme(legend.position=legend.loc)
+    }
+    return(gg)
   }
 }
 

diff --git a/cleanup b/cleanup
@@ -1,17 +1,6 @@
 #!/bin/sh
 rm -f src/Makevars configure.log autobrew
 rm -Rf .deps
-
-rm -Rf .deps
-rm -Rf .deps
-rm -Rf .deps
-rm -Rf .deps
-rm -Rf .deps
-rm -Rf .deps
-rm -Rf .deps
-rm -Rf .deps
-rm -Rf .deps
-rm -Rf .deps
 rm -Rf .deps
 rm -Rf .deps
 rm -Rf .deps

diff --git a/docs/conversion.html b/docs/conversion.html
@@ -13,7 +13,7 @@
 
 <title>Conversion</title>
 
-<script src="site_libs/header-attrs-2.26/header-attrs.js"></script>
+<script src="site_libs/header-attrs-2.27/header-attrs.js"></script>
 <script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
 <meta name="viewport" content="width=device-width, initial-scale=1" />
 <link href="site_libs/bootstrap-3.3.5/css/flatly.min.css" rel="stylesheet" />

diff --git a/docs/deconvolution.html b/docs/deconvolution.html
@@ -13,7 +13,7 @@
 
 <title>Niche Clustering</title>
 
-<script src="site_libs/header-attrs-2.26/header-attrs.js"></script>
+<script src="site_libs/header-attrs-2.27/header-attrs.js"></script>
 <script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
 <meta name="viewport" content="width=device-width, initial-scale=1" />
 <link href="site_libs/bootstrap-3.3.5/css/flatly.min.css" rel="stylesheet" />

diff --git a/docs/importingdata.html b/docs/importingdata.html
@@ -13,7 +13,7 @@
 
 <title>Importing Spatial Data</title>
 
-<script src="site_libs/header-attrs-2.26/header-attrs.js"></script>
+<script src="site_libs/header-attrs-2.27/header-attrs.js"></script>
 <script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
 <meta name="viewport" content="width=device-width, initial-scale=1" />
 <link href="site_libs/bootstrap-3.3.5/css/flatly.min.css" rel="stylesheet" />

diff --git a/docs/index.html b/docs/index.html
@@ -13,7 +13,7 @@
 
 <title>VoltRon</title>
 
-<script src="site_libs/header-attrs-2.26/header-attrs.js"></script>
+<script src="site_libs/header-attrs-2.27/header-attrs.js"></script>
 <script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
 <meta name="viewport" content="width=device-width, initial-scale=1" />
 <link href="site_libs/bootstrap-3.3.5/css/flatly.min.css" rel="stylesheet" />

diff --git a/docs/interactive.html b/docs/interactive.html
@@ -13,7 +13,7 @@
 
 <title>Interactive</title>
 
-<script src="site_libs/header-attrs-2.26/header-attrs.js"></script>
+<script src="site_libs/header-attrs-2.27/header-attrs.js"></script>
 <script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
 <meta name="viewport" content="width=device-width, initial-scale=1" />
 <link href="site_libs/bootstrap-3.3.5/css/flatly.min.css" rel="stylesheet" />

diff --git a/docs/moleculeanalysis.html b/docs/moleculeanalysis.html
@@ -13,7 +13,7 @@
 
 <title>Molecule Analysis</title>
 
-<script src="site_libs/header-attrs-2.26/header-attrs.js"></script>
+<script src="site_libs/header-attrs-2.27/header-attrs.js"></script>
 <script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
 <meta name="viewport" content="width=device-width, initial-scale=1" />
 <link href="site_libs/bootstrap-3.3.5/css/flatly.min.css" rel="stylesheet" />

diff --git a/docs/multiomic.Rmd b/docs/multiomic.Rmd
@@ -114,7 +114,7 @@ VoltRon can analyze and also integrate information from distinct spatial data ty
 
 We will first import both histological images and manual annotations using the **importImageData** function which accepts both images to generate tile/pixel level datasets but also allows one to import either a list of segments or [GeoJSON](https://geojson.org/) objects for create ROI-level datasets as separate assays in a single VoltRon layer. The .geojson file was generated using [QuPath](https://qupath.github.io/) on the same section H&E image of one Xenium section with the acute COVID-19 case. We also have to flip the coordinates of ROI annotations also for they were directly imported from QuPath which incorporates a reverse coordinate system on the y-axis.
 
-Once imported, the resulting VoltRon object will have two assays in a single layer, one for tile dataset of the H&E image and the other for ROI based annotations of again the same image.
+Once imported, the resulting VoltRon object will have two assays in a single layer, one for tile dataset of the H&E image and the other for ROI based annotations of again the same image. You can download the H&E image from [here](https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Multiomics/acutecase1_HE.jpg).
 
 ```{r eval = FALSE, class.source="watch-out"}
 # get image

diff --git a/docs/multiomic.html b/docs/multiomic.html
@@ -13,7 +13,7 @@
 
 <title>Multi-omics</title>
 
-<script src="site_libs/header-attrs-2.26/header-attrs.js"></script>
+<script src="site_libs/header-attrs-2.27/header-attrs.js"></script>
 <script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
 <meta name="viewport" content="width=device-width, initial-scale=1" />
 <link href="site_libs/bootstrap-3.3.5/css/flatly.min.css" rel="stylesheet" />
@@ -553,7 +553,9 @@ <h2>Automated H&amp;E Registration</h2>
 reverse coordinate system on the y-axis.</p>
 <p>Once imported, the resulting VoltRon object will have two assays in a
 single layer, one for tile dataset of the H&amp;E image and the other
-for ROI based annotations of again the same image.</p>
+for ROI based annotations of again the same image. You can download the
+H&amp;E image from <a
+href="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Multiomics/acutecase1_HE.jpg">here</a>.</p>
 <pre class="r watch-out"><code># get image
 imgdata &lt;- importImageData(&quot;acutecase1_HE.jpg&quot;, 
                            segments = &quot;acutecase1_membrane.geojson&quot;, 

diff --git a/docs/pixelanalysis.html b/docs/pixelanalysis.html
@@ -13,7 +13,7 @@
 
 <title>Importing Spatial Data</title>
 
-<script src="site_libs/header-attrs-2.26/header-attrs.js"></script>
+<script src="site_libs/header-attrs-2.27/header-attrs.js"></script>
 <script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
 <meta name="viewport" content="width=device-width, initial-scale=1" />
 <link href="site_libs/bootstrap-3.3.5/css/flatly.min.css" rel="stylesheet" />

diff --git a/docs/registration.html b/docs/registration.html
@@ -13,7 +13,7 @@
 
 <title>Image Registration</title>
 
-<script src="site_libs/header-attrs-2.26/header-attrs.js"></script>
+<script src="site_libs/header-attrs-2.27/header-attrs.js"></script>
 <script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
 <meta name="viewport" content="width=device-width, initial-scale=1" />
 <link href="site_libs/bootstrap-3.3.5/css/flatly.min.css" rel="stylesheet" />

diff --git a/docs/roianalysis.html b/docs/roianalysis.html
@@ -13,7 +13,7 @@
 
 <title>ROI Analysis</title>
 
-<script src="site_libs/header-attrs-2.26/header-attrs.js"></script>
+<script src="site_libs/header-attrs-2.27/header-attrs.js"></script>
 <script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
 <meta name="viewport" content="width=device-width, initial-scale=1" />
 <link href="site_libs/bootstrap-3.3.5/css/flatly.min.css" rel="stylesheet" />

diff --git a/docs/site_libs/header-attrs-2.27/header-attrs.js b/docs/site_libs/header-attrs-2.27/header-attrs.js
@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});
diff --git a/docs/spotanalysis.html b/docs/spotanalysis.html
@@ -13,7 +13,7 @@
 
 <title>Cell/Spot Analysis</title>
 
-<script src="site_libs/header-attrs-2.26/header-attrs.js"></script>
+<script src="site_libs/header-attrs-2.27/header-attrs.js"></script>
 <script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
 <meta name="viewport" content="width=device-width, initial-scale=1" />
 <link href="site_libs/bootstrap-3.3.5/css/flatly.min.css" rel="stylesheet" />

diff --git a/docs/tutorials.html b/docs/tutorials.html
@@ -13,7 +13,7 @@
 
 <title>Tutorials</title>
 
-<script src="site_libs/header-attrs-2.26/header-attrs.js"></script>
+<script src="site_libs/header-attrs-2.27/header-attrs.js"></script>
 <script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
 <meta name="viewport" content="width=device-width, initial-scale=1" />
 <link href="site_libs/bootstrap-3.3.5/css/flatly.min.css" rel="stylesheet" />
@@ -562,7 +562,8 @@ <h2>Other Utilities</h2>
 <img width="80%" height="80%" src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/conversion.png" class="center">
 <br> <br>
 <p style="margin: 3%">
-Converting VoltRon objects into Seurat, Squidpy (anndata) etc. </strong>
+Converting VoltRon objects into Seurat,de Squidpy (anndata) etc.
+</strong>
 </p>
 </td>
 </tr>

diff --git a/docs/voltronobjects.html b/docs/voltronobjects.html
@@ -13,7 +13,7 @@
 
 <title>Importing Spatial Data</title>
 
-<script src="site_libs/header-attrs-2.26/header-attrs.js"></script>
+<script src="site_libs/header-attrs-2.27/header-attrs.js"></script>
 <script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
 <meta name="viewport" content="width=device-width, initial-scale=1" />
 <link href="site_libs/bootstrap-3.3.5/css/flatly.min.css" rel="stylesheet" />

diff --git a/src/Makevars.win b/src/Makevars.win
@@ -1,20 +1,14 @@
-VERSION = 4.7.0
-RWINLIB = ../windows/opencv-$(VERSION)
+RWINLIB = ../windows/opencv
 PKG_CPPFLAGS = -I$(RWINLIB)/include/opencv4 -DHAVE_XFEATURES2D
-TARGET = lib$(subst gcc,,$(COMPILED_BY))$(R_ARCH)
+OLDLIBDIR = lib${subst gcc,,${COMPILED_BY}}${R_ARCH}
 
 PKG_LIBS = \
-  $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) \
-	-L$(RWINLIB)/$(TARGET) \
-	-L$(RWINLIB)/lib$(R_ARCH) \
-	-lopencv_ml470 -lopencv_objdetect470 -lopencv_photo470 -lopencv_stitching470 \
-	-lopencv_video470 -lopencv_calib3d470 -lopencv_xfeatures2d470 -lopencv_features2d470 -lopencv_highgui470 -lopencv_flann470 \
-	-lopencv_videoio470 -lopencv_imgcodecs470 -lopencv_imgproc470 -lopencv_core470 -llibopenjp2 -lquirc -ltbb \
-	-ljpeg -lwebp -lpng -lz -ltiff \
-	-lcomctl32 -lgdi32 -lole32 -lsetupapi -lws2_32 -lavifil32 -lavicap32 -lwinmm -lmsvfw32 \
-	-lopengl32 -lglu32 -lcomdlg32 -lOleAut32 -luuid
-
-CXX_STD=CXX11
+	-L$(RWINLIB)/$(OLDLIBDIR) \
+	-L$(RWINLIB)/lib \
+	-lopencv_ml481 -lopencv_objdetect481 -lopencv_photo481 -lopencv_stitching481 -lopencv_shape481 -lopencv_wechat_qrcode481 -lopencv_dnn481 \
+	-lopencv_video481 -lopencv_calib3d481 -lopencv_xfeatures2d481 -lopencv_features2d481 -lopencv_highgui481 -lopencv_flann481 \
+	-lopencv_videoio481 -lopencv_imgcodecs481 -lopencv_imgproc481 -lopencv_core481 -llibopenjp2 -lquirc \
+	-ljpeg -lwebp -lsharpyuv -lpng -lz -ltiff -lpthread -lgdi32 -lole32 -lopengl32 -lcomdlg32 -lOleAut32 -luuid
 
 all: clean winlibs
 
@@ -24,4 +18,4 @@ clean:
 winlibs:
 	"${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" "../tools/winlibs.R" ${VERSION}
 	mkdir -p ../inst
-	cp -r $(RWINLIB)/share ../inst/
+	cp -r $(RWINLIB)/share ../inst/
diff --git a/src/manual_registration.cpp b/src/manual_registration.cpp
diff --git a/tools/winlibs.R b/tools/winlibs.R
@@ -1,12 +1,18 @@
-# We need https
-if(getRversion() < "3.3.0") setInternet2()
-VERSION <- commandArgs(TRUE)
-
-# Downloads libssh2 + dependencies
-options(timeout = 400)
-if(!file.exists(sprintf("../windows/opencv-%s/include/opencv4/opencv2/opencv.hpp", VERSION))){
-  download.file(sprintf("https://github.com/rwinlib/opencv/archive/v%s.zip", VERSION), "lib.zip", quiet = TRUE)
+if(!file.exists("../windows/opencv/include/opencv4/opencv2/opencv.hpp")){
+  unlink("../windows", recursive = TRUE)
+  url <- if(grepl("aarch", R.version$platform)){
+    "https://github.com/r-windows/bundles/releases/download/opencv-4.8.1/opencv-4.8.1-clang-aarch64.tar.xz"
+  } else if(grepl("clang", Sys.getenv('R_COMPILED_BY'))){
+    "https://github.com/r-windows/bundles/releases/download/opencv-4.8.1/opencv-4.8.1-clang-x86_64.tar.xz"
+  } else if(getRversion() >= "4.3") {
+    "https://github.com/r-windows/bundles/releases/download/opencv-4.8.1/opencv-4.8.1-ucrt-x86_64.tar.xz"
+  } else {
+    "https://github.com/rwinlib/opencv/archive/refs/tags/v4.8.1.tar.gz"
+  }
+  download.file(url, basename(url), quiet = TRUE)
   dir.create("../windows", showWarnings = FALSE)
-  unzip("lib.zip", exdir = "../windows")
-  unlink("lib.zip")
-}
+  untar(basename(url), exdir = "../windows", tar = 'internal')
+  unlink(basename(url))
+  setwd("../windows")
+  file.rename(list.files(), 'opencv')
+}